| Sonstiges: |
- Nachgewiesen in: MEDLINE
- Sprachen: English
- Publication Type: Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't
- Language: English
- [Mol Syst Biol] 2024 May; Vol. 20 (5), pp. 481-505. <i>Date of Electronic Publication: </i>2024 Feb 14.
- MeSH Terms: Catechol O-Methyltransferase* / genetics ; Catechol O-Methyltransferase* / metabolism ; Machine Learning* ; Polymorphism, Single Nucleotide* ; Humans ; RNA, Messenger / genetics ; RNA, Messenger / metabolism ; Ribosomes / metabolism ; Ribosomes / genetics ; Protein Biosynthesis
- Comments: Update of: bioRxiv. 2023 Nov 17;:. (PMID: 38014045)
- References: Andrews S, Snowflack DR, Clark IE, Gavis ER (2011) Multiple mechanisms collaborate to repress nanos translation in the Drosophila ovary and embryo. RNA 17:967–977. (PMID: 21460235307874510.1261/rna.2478611) ; Battle A, Khan Z, Wang SH, Mitrano A, Ford MJ, Pritchard JK, Gilad Y (2015) Genomic variation. Impact of regulatory variation from RNA to protein. Science 347:664–667. (PMID: 2565724910.1126/science.1260793) ; Bazzini AA, del Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, Yao J, Khokha MK, Giraldez AJ (2016) Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J 35:2087–2103. (PMID: 27436874504834710.15252/embj.201694699) ; Behrens A, Rodschinka G, Nedialkova DD (2021) High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq. Mol Cell 81:1802-1815.e7. (PMID: 33581077806279010.1016/j.molcel.2021.01.028) ; Benoit Bouvrette LP, Bovaird S, Blanchette M, Lécuyer E (2020) oRNAment: a database of putative RNA binding protein target sites in the transcriptomes of model species. Nucleic Acids Res 48:D166–D173. (PMID: 31724725) ; Bialecka M, Kurzawski M, Klodowska-Duda G, Opala G, Tan E-K, Drozdzik M (2008) The association of functional catechol-O-methyltransferase haplotypes with risk of Parkinson’s disease, levodopa treatment response, and complications. Pharmacogenet Genomics 18:815–821. (PMID: 1869823410.1097/FPC.0b013e328306c2f2) ; Bodenhofer U, Kothmeier A, Hochreiter S (2011) APCluster: an R package for affinity propagation clustering. Bioinformatics 27:2463–2464. (PMID: 2173743710.1093/bioinformatics/btr406) ; Braat AK, Yan N, Arn E, Harrison D, Macdonald PM (2004) Localization-dependent oskar protein accumulation; control after the initiation of translation. Dev Cell 7:125–131. (PMID: 1523996010.1016/j.devcel.2004.06.009) ; Brandes N, Goldman G, Wang CH, Ye CJ, Ntranos V (2023) Genome-wide prediction of disease variant effects with a deep protein language model. Nat Genet 55:1512–1522. (PMID: 375633291048479010.1038/s41588-023-01465-0) ; Bray NJ, Buckland PR, Williams NM, Williams HJ, Norton N, Owen MJ, O’Donovan MC (2003) A haplotype implicated in schizophrenia susceptibility is associated with reduced COMT expression in human brain. Am J Hum Genet 73:152–161. (PMID: 12802784118057610.1086/376578) ; Burke PC, Park H, Subramaniam AR (2022) A nascent peptide code for translational control of mRNA stability in human cells. Nat Commun 13:6829. (PMID: 36369503965222610.1038/s41467-022-34664-0) ; Cenik C, Cenik ES, Byeon GW, Grubert F, Candille SI, Spacek D, Alsallakh B, Tilgner H, Araya CL, Tang H et al (2015) Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res 25:1610–1621. (PMID: 26297486461795810.1101/gr.193342.115) ; Chen J, Lipska BK, Halim N, Ma QD, Matsumoto M, Melhem S, Kolachana BS, Hyde TM, Herman MM, Apud J et al (2004) Functional analysis of genetic variation in catechol-O-methyltransferase (COMT): effects on mRNA, protein, and enzyme activity in postmortem human brain Am J Hum Genet 75:807–821. (PMID: 15457404118211010.1086/425589) ; Cheng CY, Kladwang W, Yesselman JD, Das R (2017) RNA structure inference through chemical mapping after accidental or intentional mutations. Proc Natl Acad Sci USA 114:9876–9881. (PMID: 28851837560399010.1073/pnas.1619897114) ; Chiasson MA, Rollins NJ, Stephany JJ, Sitko KA, Matreyek KA, Verby M, Sun S, Roth FP, DeSloover D, Marks DS et al (2020) Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact. Elife 9:e58026. (PMID: 32870157746261310.7554/eLife.58026) ; Clark IE, Wyckoff D, Gavis ER (2000) Synthesis of the posterior determinant Nanos is spatially restricted by a novel cotranslational regulatory mechanism. Curr Biol 10:1311–1314. (PMID: 1106911610.1016/S0960-9822(00)00754-5) ; Costantini LM, Baloban M, Markwardt ML, Rizzo M, Guo F, Verkhusha VV, Snapp EL (2015) A palette of fluorescent proteins optimized for diverse cellular environments. Nat Commun 6:7670. (PMID: 26158227449987010.1038/ncomms8670) ; Dawling S, Roodi N, Mernaugh RL, Wang X, Parl FF (2001) Catechol-O-methyltransferase (COMT)-mediated metabolism of catechol estrogens: comparison of wild-type and variant COMT isoforms. Cancer Res 61:6716–6722. (PMID: 11559542) ; DeLano WL (2002) Pymol: an open-source molecular graphics tool. CCP4 Newsl Protein Crystallogr 40: 82–92. ; Egan MF, Goldberg TE, Kolachana BS, Callicott JH, Mazzanti CM, Straub RE, Goldman D, Weinberger DR (2001) Effect of COMT Val108/158 Met genotype on frontal lobe function and risk for schizophrenia. Proc Natl Acad Sci USA 98:6917–6922. (PMID: 113811113445310.1073/pnas.111134598) ; Esposito D, Weile J, Shendure J, Starita LM, Papenfuss AT, Roth FP, Fowler DM, Rubin AF (2019) MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect. Genome Biol 20:223. https://doi.org/10.1186/s13059-019-1845-6. ; Faure AJ, Domingo J, Schmiedel JM, Hidalgo-Carcedo C, Diss G, Lehner B (2022) Mapping the energetic and allosteric landscapes of protein binding domains. Nature 604:175–183. (PMID: 3538819210.1038/s41586-022-04586-4) ; Fernandes AD, Macklaim JM, Linn TG, Reid G (2013) ANOVA-like differential gene expression analysis of single-organism and meta-RNA-seq. PLoS ONE 8(7):e67019. (PMID: 23843979369959110.1371/journal.pone.0067019) ; Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, Edgell DR, Gloor GB (2014) Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis. Microbiome 2:15. (PMID: 24910773403073010.1186/2049-2618-2-15) ; Findlay GM, Daza RM, Martin B, Zhang MD, Leith AP, Gasperini M, Janizek JD, Huang X, Starita LM, Shendure J (2018) Accurate classification of BRCA1 variants with saturation genome editing. Nature 562:217–222. (PMID: 30209399618177710.1038/s41586-018-0461-z) ; Floor SN, Doudna JA (2016) Tunable protein synthesis by transcript isoforms in human cells. Elife 5:e10921. (PMID: 26735365476458310.7554/eLife.10921) ; Fotsis T, Zhang Y, Pepper MS, Adlercreutz H, Montesano R, Nawroth PP, Schweigerer L (1994) The endogenous oestrogen metabolite 2-methoxyoestradiol inhibits angiogenesis and suppresses tumour growth. Nature 368:237–239. (PMID: 751179810.1038/368237a0) ; Fowler DM, Araya CL, Fleishman SJ, Kellogg EH, Stephany JJ, Baker D, Fields S (2010) High-resolution mapping of protein sequence-function relationships. Nat Methods 7:741–746. (PMID: 20711194293887910.1038/nmeth.1492) ; Frey BJ, Dueck D (2007) Clustering by passing messages between data points. Science 315:972–976. (PMID: 1721849110.1126/science.1136800) ; Gamble CE, Brule CE, Dean KM, Fields S, Grayhack EJ (2016) Adjacent codons act in concert to modulate translation efficiency in yeast. Cell 166:679–690. (PMID: 27374328496701210.1016/j.cell.2016.05.070) ; Gloor G (2021) Measuring effect size in ALDEx2. Gloor lab musings. https://gloorlab.blogspot.com/2021/03/measuring-effect-size-in-aldex2.html. ; Gloor GB, Macklaim JM, Fernandes AD (2016) Displaying variation in large datasets: plotting a visual summary of effect sizes. J Comput Graph Stat 25:971–979. (PMID: 10.1080/10618600.2015.1131161) ; Gogakos T, Brown M, Garzia A, Meyer C, Hafner M, Tuschl T (2017) Characterizing expression and processing of precursor and mature human tRNAs by Hydro-tRNAseq and PAR-CLIP. Cell Rep 20:1463–1475. https://doi.org/10.1016/j.celrep.2017.07.029. (PMID: 10.1016/j.celrep.2017.07.029287932685564215) ; Greenacre M (2021) Compositional data analysis. Annu Rev Stat Appl 8:271–299. (PMID: 10.1146/annurev-statistics-042720-124436) ; Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70–4. (PMID: 18424795244780910.1093/nar/gkn188) ; GTEx Consortium (2020) The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science 369:1318–1330. (PMID: 10.1126/science.aaz1776) ; Guillot CR, Fanning JR, Liang T, Berman ME (2015) COMT associations with disordered gambling and drinking measures. J Gambl Stud 31:513–524. (PMID: 24390676408247810.1007/s10899-013-9434-1) ; Hashimoto Y, Shiina M, Maekawa S, Kato T, Shahryari V, Kulkarni P, Dasgupta P, Yamamura S, Saini S, Tabatabai ZL et al (2021) Suppressor effect of catechol-O-methyltransferase gene in prostate cancer. PLoS ONE 16:e0253877. (PMID: 34587154848083910.1371/journal.pone.0253877) ; Hendershot CS, Lindgren KP, Liang T, Hutchison KE (2012) COMT and ALDH2 polymorphisms moderate associations of implicit drinking motives with alcohol use. Addict Biol 17:192–201. https://doi.org/10.1111/j.1369-1600.2010.00286.x. (PMID: 10.1111/j.1369-1600.2010.00286.x21309949) ; Hoskins I (2023) satmut_utils: v1.0.3-dev001. Zenodo. ; Hoskins I, Sun S, Cote A, Roth FP, Cenik C (2023) satmut_utils: a simulation and variant calling package for multiplexed assays of variant effect. Genome Biol 24:1–27. (PMID: 10.1186/s13059-023-02922-z) ; Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802. (PMID: 22056041322528810.1016/j.cell.2011.10.002) ; Janacova L, Stenckova M, Lapcik P, Hrachovinova S, Bouchalova P, Potesil D, Hrstka R, Müller P, Bouchal P (2023) Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer. Sci Rep 13:1285. (PMID: 36690660987091110.1038/s41598-023-28078-1) ; Karczewski KJ, Francioli LC, Tiao G, Cummings BB, Alföldi J, Wang Q, Collins RL, Laricchia KM, Ganna A, Birnbaum DP et al (2020) The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581:434–443. (PMID: 32461654733419710.1038/s41586-020-2308-7) ; Kimchi-Sarfaty C, Oh JM, Kim I-W, Sauna ZE, Calcagno AM, Ambudkar SV, Gottesman MM (2007) A ‘silent’ polymorphism in the MDR1 gene changes substrate specificity. Science 315:525–528. (PMID: 1718556010.1126/science.1135308) ; Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N (2019) Saturation mutagenesis of twenty disease-associated regulatory elements at single base-pair resolution. Nat Commun 10:3583. (PMID: 31395865668789110.1038/s41467-019-11526-w) ; Kirchner S, Cai Z, Rauscher R, Kastelic N, Anding M, Czech A, Kleizen B, Ostedgaard LS, Braakman I, Sheppard DN et al (2017) Alteration of protein function by a silent polymorphism linked to tRNA abundance. PLoS Biol 15:e2000779. (PMID: 28510592543368510.1371/journal.pbio.2000779) ; Kladwang W, Cordero P, Das R (2011) A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. RNA 17:522–534. (PMID: 21239468303915110.1261/rna.2516311) ; Kladwang W, Das R (2010) A mutate-and-map strategy for inferring base pairs in structured nucleic acids: proof of concept on a DNA/RNA helix. Biochemistry 49:7414–7416. (PMID: 2067778010.1021/bi101123g) ; Klauber N, Parangi S, Flynn E, Hamel E, D’Amato RJ (1997) Inhibition of angiogenesis and breast cancer in mice by the microtubule inhibitors 2-methoxyestradiol and taxol. Cancer Res 57:81–86. (PMID: 8988045) ; Kohonen T (1982) Self-organized formation of topologically correct feature maps. Biol Cybern 43:59–69. (PMID: 10.1007/BF00337288) ; Kwong A, Boughton AP, Wang M, VandeHaar P, Boehnke M, Abecasis G, Kang HM (2022) FIVEx: an interactive eQTL browser across public datasets. Bioinformatics 38:559–561. (PMID: 3445987210.1093/bioinformatics/btab614) ; Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, Gu B, Hart J, Hoffman D, Hoover J et al (2016) ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44:D862–8. (PMID: 2658291810.1093/nar/gkv1222) ; Lappalainen T, Sammeth M, Friedländer MR, ’t Hoen PAC, Monlong J, Rivas MA, Gonzàlez-Porta M, Kurbatova N, Griebel T, Ferreira PG et al (2013) Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501:506–511. (PMID: 24037378391845310.1038/nature12531) ; Larsen FB, Cagiada M, Dideriksen J, Stein A, Lindorff-Larsen K, Hartmann-Petersen R (2023) Rare catechol-O-methyltransferase missense variants are structurally unstable proteasome targets. Biochemistry 62:1394–1405. (PMID: 3697627110.1021/acs.biochem.3c00008) ; Leek JT, Johnson WE, Parker HS, Fertig EJ, Jaffe AE, Zhang Y, Storey JD, Torres LC (2022) sva: Surrogate Variable Analysis. R package version 3.46.0. https://bioconductor.org/packages/sva. ; Li P, Zhou X, Xu K, Zhang QC (2021) RASP: an atlas of transcriptome-wide RNA secondary structure probing data. Nucleic Acids Res 49:D183–D191. (PMID: 3306841210.1093/nar/gkaa880) ; Li Q, Makri A, Lu Y, Marchand L, Grabs R, Rousseau M, Ounissi-Benkalha H, Pelletier J, Robert F, Harmsen E et al (2013) Genome-wide search for exonic variants affecting translational efficiency. Nat Commun 4:2260. (PMID: 2390016810.1038/ncomms3260) ; Li Z, Chen L (2023) Predicting functional consequences of SNPs on mRNA translation via machine learning. Nucleic Acids Res 51:7868–7881. (PMID: 374277811045016910.1093/nar/gkad576) ; Lim Y, Arora S, Schuster SL, Corey L, Fitzgibbon M, Wladyka CL, Wu X, Coleman IM, Delrow JJ, Corey E et al (2021) Multiplexed functional genomic analysis of 5’untranslated region mutations across the spectrum of prostate cancer. Nat Commun 12:1–18. (PMID: 10.1038/s41467-021-24445-6) ; Lin C-H, Ray Chaudhuri K, Fan J-Y, Ko C-I, Rizos A, Chang C-W, Lin H-I, Wu Y-R (2017) Depression and catechol-O-methyltransferase (COMT) genetic variants are associated with pain in Parkinson’s disease. Sci Rep 7:6306. https://doi.org/10.1038/s41598-017-06782-z. ; Lloyd JPB, French CE, Brenner SE (2020) Polysome fractionation analysis reveals features important for human nonsense-mediated mRNA decay. Preprint at https://doi.org/10.1101/2020.03.08.981811. ; Majithia AR, Tsuda B, Agostini M, Gnanapradeepan K, Rice R, Peloso G, Patel KA, Zhang X, Broekema MF, Patterson N et al (2016) Prospective functional classification of all possible missense variants in PPARG. Nat Genet 48:1570–1575. (PMID: 27749844513184410.1038/ng.3700) ; Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ et al (2018) Multiplex assessment of protein variant abundance by massively parallel sequencing. Nat Genet 50:874–882. (PMID: 29785012598076010.1038/s41588-018-0122-z) ; Matreyek KA, Stephany JJ, Chiasson MA, Hasle N, Fowler DM (2020) An improved platform for functional assessment of large protein libraries in mammalian cells. Nucleic Acids Res 48:e1. (PMID: 31612958) ; Matreyek KA, Stephany JJ, Fowler DM (2017) A platform for functional assessment of large variant libraries in mammalian cells. Nucleic Acids Res 45:e102. (PMID: 28335006549981710.1093/nar/gkx183) ; Mauger DM, Cabral BJ, Presnyak V, Su SV, Reid DW, Goodman B, Link K, Khatwani N, Reynders J, Moore MJ et al (2019) mRNA structure regulates protein expression through changes in functional half-life. Proc Natl Acad Sci USA 116:24075–24083. (PMID: 31712433688384810.1073/pnas.1908052116) ; May GE, Akirtava C, Agar-Johnson M, Micic J, Woolford J, McManus J (2023) Unraveling the influences of sequence and position on yeast uORF activity using massively parallel reporter systems and machine learning. Elife 12:e69611. (PMID: 372270541025949310.7554/eLife.69611) ; Meyer-Lindenberg A, Nichols T, Callicott JH, Ding J, Kolachana B, Buckholtz J, Mattay VS, Egan M, Weinberger DR (2006) Impact of complex genetic variation in COMT on human brain function. Mol Psychiatry 11:867–77. 797. (PMID: 1678603210.1038/sj.mp.4001860) ; Michel AM, Fox G, M Kiran A, De Bo C, O’Connor PBF, Heaphy SM, Mullan JPA, Donohue CA, Higgins DG, Baranov PV (2014) GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res 42:D859–64. (PMID: 2418569910.1093/nar/gkt1035) ; Mukhopadhyay T, Roth JA (1998) Superinduction of wild-type p53 protein after 2-methoxyestradiol treatment of Ad5p53-transduced cells induces tumor cell apoptosis. Oncogene 17:241–246. (PMID: 967470910.1038/sj.onc.1201909) ; Munro D, Singh M (2020) DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction. Bioinformatics 36(22-23):5322–5329. (PMID: 801645410.1093/bioinformatics/btaa1030) ; Nackley AG, Shabalina SA, Lambert JE, Conrad MS, Gibson DG, Spiridonov AN, Satterfield SK, Diatchenko L (2009) Low enzymatic activity haplotypes of the human catechol-O-methyltransferase gene: enrichment for marker SNPs. PLoS ONE 4:e5237. (PMID: 19365560266492710.1371/journal.pone.0005237) ; Nackley AG, Shabalina SA, Tchivileva IE, Satterfield K, Korchynskyi O, Makarov SS, Maixner W, Diatchenko L (2006) Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 314:1930–1933. (PMID: 1718560110.1126/science.1131262) ; Narula A, Ellis J, Taliaferro JM, Rissland OS (2019) Coding regions affect mRNA stability in human cells. RNA 25:1751–1764. (PMID: 31527111685985010.1261/rna.073239.119) ; Ozadam H, Geng M, Cenik C (2020) RiboFlow, RiboR and RiboPy: an ecosystem for analyzing ribosome profiling data at read length resolution. Bioinformatics 36:2929–2931. (PMID: 31930375720375510.1093/bioinformatics/btaa028) ; Picardi E, D’Erchia AM, Lo Giudice C, Pesole G (2017) REDIportal: a comprehensive database of A-to-I RNA editing events in humans. Nucleic Acids Res 45:D750–D757. (PMID: 2758758510.1093/nar/gkw767) ; Presnyak V, Alhusaini N, Chen Y-H, Martin S, Morris N, Kline N, Olson S, Weinberg D, Baker KE, Graveley BR et al (2015) Codon optimality is a major determinant of mRNA stability. Cell 160:1111–1124. (PMID: 25768907435974810.1016/j.cell.2015.02.029) ; Qian X-K, Wang P, Xia Y-L, Dou T-Y, Jin Q, Wang D-D, Hao D-C, Bi X-L, Ge G-B, Yang L (2016) A highly selective fluorescent probe for sensing activities of catechol- O -methyltransferase in complex biological samples. Sens Actuators B Chem 231:615–623. https://doi.org/10.1016/j.snb.2016.03.074. (PMID: 10.1016/j.snb.2016.03.074) ; Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D et al (2023) JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Res 52(D1):D174–D182. (PMID: 1076780910.1093/nar/gkad1059) ; Richter JD, Coller J (2015) Pausing on polyribosomes: make way for elongation in translational control. Cell 163:292–300. (PMID: 26451481460012810.1016/j.cell.2015.09.041) ; Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK (2015) limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43:e47. (PMID: 25605792440251010.1093/nar/gkv007) ; Rouskin S, Zubradt M, Washietl S, Kellis M, Weissman JS (2014) Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo. Nature 505:701–705. (PMID: 2433621410.1038/nature12894) ; Rubin AF, Gelman H, Lucas N, Bajjalieh SM, Papenfuss AT, Speed TP, Fowler DM (2017) A statistical framework for analyzing deep mutational scanning data. Genome Biol 18:150. (PMID: 28784151554749110.1186/s13059-017-1272-5) ; Ruottinen HM, Rinne UK (1998) COMT inhibition in the treatment of Parkinson’s disease. J Neurol 245:P25–P34. https://doi.org/10.1007/pl00007743. (PMID: 10.1007/pl000077439808337) ; Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J (2013a) RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Hum Mutat 34:546–556. (PMID: 23315997370810710.1002/humu.22273) ; Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J (2013b) The RNAsnp web server: predicting SNP effects on local RNA secondary structure. Nucleic Acids Res 41:W475–W479. ; Sambrook J, Russell DW (2006) Isolation of DNA fragments from polyacrylamide gels by the crush and soak method. CSH Protoc 2006:pdb.prot2936. (PMID: 22485254) ; Sample PJ, Wang B, Reid DW, Presnyak V, McFadyen IJ, Morris DR, Seelig G (2019) Human 5’ UTR design and variant effect prediction from a massively parallel translation assay. Nat Biotechnol 37:803–809. (PMID: 31267113710013310.1038/s41587-019-0164-5) ; Schott BH, Frischknecht R, Debska-Vielhaber G, John N, Behnisch G, Düzel E, Gundelfinger ED, Seidenbecher CI (2010) Membrane-bound catechol-O-methyl transferase in cortical neurons and glial cells is intracellularly oriented. Front Psychiatry 1:142. (PMID: 21423451305965110.3389/fpsyt.2010.00142) ; Sei Y, Li Z, Song J, Ren-Patterson R, Tunbridge EM, Iizuka Y, Inoue M, Alfonso BT, Beltaifa S, Nakai Y et al (2010) Epistatic and functional interactions of catechol-o-methyltransferase (COMT) and AKT1 on neuregulin1-ErbB signaling in cell models. PLoS ONE 5:e10789. (PMID: 20520724287539110.1371/journal.pone.0010789) ; Shifman S, Bronstein M, Sternfeld M, Pisanté-Shalom A, Lev-Lehman E, Weizman A, Reznik I, Spivak B, Grisaru N, Karp L et al (2002) A highly significant association between a COMT haplotype and schizophrenia. Am J Hum Genet 71:1296–1302. (PMID: 1240221737856710.1086/344514) ; Simhadri VL, Hamasaki-Katagiri N, Lin BC, Hunt R, Jha S, Tseng SC, Wu A, Bentley AA, Zichel R, Lu Q et al (2017) Single synonymous mutation in factor IX alters protein properties and underlies haemophilia B. J Med Genet 54:338–345. (PMID: 2800793910.1136/jmedgenet-2016-104072) ; Starita LM, Young DL, Islam M, Kitzman JO, Gullingsrud J, Hause RJ, Fowler DM, Parvin JD, Shendure J, Fields S (2015) Massively parallel functional analysis of BRCA1 RING domain variants. Genetics 200:413–422. (PMID: 25823446449236810.1534/genetics.115.175802) ; Starr TN, Greaney AJ, Hilton SK, Ellis D, Crawford KHD, Dingens AS, Navarro MJ, Bowen JE, Tortorici MA, Walls AC et al (2020) Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding. Cell 182:1295-1310.e20. (PMID: 32841599741870410.1016/j.cell.2020.08.012) ; Suiter CC, Moriyama T, Matreyek KA, Yang W, Scaletti ER, Nishii R, Yang W, Hoshitsuki K, Singh M, Trehan A et al (2020) Massively parallel variant characterization identifies NUDT15 alleles associated with thiopurine toxicity. Proc Natl Acad Sci USA 117:5394–5401. (PMID: 32094176707189310.1073/pnas.1915680117) ; Sun S, Yang F, Tan G, Costanzo M, Oughtred R, Hirschman J, Theesfeld CL, Bansal P, Sahni N, Yi S et al (2016) An extended set of yeast-based functional assays accurately identifies human disease mutations. Genome Res 26:670–680. https://doi.org/10.1101/gr.192526.115. (PMID: 10.1101/gr.192526.115269757784864455) ; Tan G, Lenhard B (2016) TFBSTools: an R/bioconductor package for transcription factor binding site analysis. Bioinformatics 32:1555–1556. (PMID: 26794315486652410.1093/bioinformatics/btw024) ; Tesina P, Lessen LN, Buschauer R, Cheng J, Wu CC-C, Berninghausen O, Buskirk AR, Becker T, Beckmann R, Green R (2020) Molecular mechanism of translational stalling by inhibitory codon combinations and poly(A) tracts. EMBO J 39:e103365. (PMID: 3185861410.15252/embj.2019103365) ; Tsao D, Shabalina SA, Gauthier J, Dokholyan NV, Diatchenko L (2011) Disruptive mRNA folding increases translational efficiency of catechol-O-methyltransferase variant. Nucleic Acids Res 39:6201–6212. (PMID: 21486747315232810.1093/nar/gkr165) ; Wehrens R, Buydens LMC (2007) Self- and super-organizing maps in R: the Kohonen package. J Stat Softw 21:1–19. (PMID: 10.18637/jss.v021.i05) ; Weile J, Sun S, Cote AG, Knapp J, Verby M, Mellor JC, Wu Y, Pons C, Wong C, van Lieshout N et al (2017) A framework for exhaustively mapping functional missense variants. Mol Syst Biol 13:957. (PMID: 29269382574049810.15252/msb.20177908) ; Weng X, Gong J, Chen Y, Wu T, Wang F, Yang S, Yuan Y, Luo G, Chen K, Hu L et al (2020) Keth-seq for transcriptome-wide RNA structure mapping. Nat Chem Biol 16:489–492. (PMID: 32015521718249210.1038/s41589-019-0459-3) ; Wu Q, Medina SG, Kushawah G, DeVore ML, Castellano LA, Hand JM, Wright M, Bazzini AA (2019) Translation affects mRNA stability in a codon-dependent manner in human cells. Elife 8:e45396. (PMID: 31012849652921610.7554/eLife.45396) ; Wu X, Bartel DP (2017) Widespread influence of 3’-end structures on mammalian mRNA processing and stability. Cell 169:905-917.e11. (PMID: 28525757554674410.1016/j.cell.2017.04.036) ; Zhang S, Hu H, Zhou J, He X, Jiang T, Zeng J (2017) Analysis of ribosome stalling and translation elongation dynamics by deep learning. Cell Syst 5:212-220.e6. (PMID: 2895765510.1016/j.cels.2017.08.004) ; Zheng Z, Liebers M, Zhelyazkova B, Cao Y, Panditi D, Lynch KD, Chen J, Robinson HE, Shim HS, Chmielecki J et al (2014) Anchored multiplex PCR for targeted next-generation sequencing. Nat Med 20:1479–1484. (PMID: 2538408510.1038/nm.3729) ; Zubradt M, Gupta P, Persad S, Lambowitz AM, Weissman JS, Rouskin S (2017) DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat Methods 14:75–82. (PMID: 2781966110.1038/nmeth.4057)
- Grant Information: R35 GM150667 United States GM NIGMS NIH HHS
- Contributed Indexing: Keywords: COMT; MAVE; Mutagenesis; RNA Secondary Structure; Ribosome Load
- Substance Nomenclature: EC 2.1.1.6 (Catechol O-Methyltransferase) ; EC 2.1.1.6 (COMT protein, human) ; 0 (RNA, Messenger)
- Entry Date(s): Date Created: 20240215 Date Completed: 20240502 Latest Revision: 20240521
- Update Code: 20240521
- PubMed Central ID: PMC11066095
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